source('gatc.r')
summary(t(gi.id49175990.gatc))
t(gi.id49175990.gatc)[1,1]
hist(t(gi.id49175990.gatc))
gd=read.table('gatcdist.txt')
hist(gd)
hist(gd$V1)
(gd$V1)
hist(gd$V1)
gd=read.table('gatcdist.txt')
hist(gd$V1)
hist(gd$V1,breaks=100)
hist(gd$V1,breaks=1000)
hist(gd$V1,breaks=10000)
summary(gd$V1)
hist(gd$V1,breaks=100)
hist(gd$V1,breaks=10)
hist(gd$V1,breaks=100)
plot(density(s[s$V1>60,]$V2),col="black",xlab="Position on Longest Celera Scaffold",main="Snapper2 mapped Illumina Reads (at different match percent)",ylab="Density of Reads")
plot(density(gd$V1),col="black",xlab="Position on Longest Celera Scaffold",main="Snapper2 mapped Illumina Reads (at different match percent)",ylab="Density of Reads")
hist(gd$V1,breaks=100)
plot(density(gd$V1),col="black",xlab="Position on Longest Celera Scaffold",main="Snapper2 mapped Illumina Reads (at different match percent)",ylab="Density of Reads")
x=c(1 3 5 7 9 11)
x=c(1,3,5,7,9,11)
fft(x)
plot(fft(x))
hist(gd$V1,breaks=100)
gd=read.table('data/gi.id=157154711.gatc.gd')
hist(gd$V1,breaks=100)
gd157154711=read.table('data/gi.id=157154711.gatc.gd')
gd117622295=read.table('data/gi.id=117622295.gatc.gd')
gd157159467=read.table('data/gi.id=157159467.gatc.gd')
gd15829254=read.table('data/gi.id=15829254.gatc.gd')
gd215485161=read.table('data/gi.id=215485161.gatc.gd')
gd218693476=read.table('data/gi.id=218693476.gatc.gd')
gd332341332=read.table('data/gi.id=332341332.gatc.gd')
gd49175990=read.table('data/gi.id=49175990.gatc.gd')
plot(density(gd$V1),col="black",xlab="Position on Longest Celera Scaffold",main="Snapper2 mapped Illumina Reads (at different match percent)",ylab="Density of Reads")
plot(density(gd$V1),col="black",xlab="Distance between successive GATC",ylab="Density of successive GATC with this distance")
lines(density(gd157154711$V1),col="green")
plot(density(gd157154711$V1),col="black",xlab="Distance between successive GATC",ylab="Density of successive GATC with this distance")
lines(density(gd117622295$V1),col="green")
lines(density(gd157159467$V1),col="red")
lines(density(gd15829254$V1),col="blue")
lines(density(gd215485161$V1),col="cyan")
lines(density(gd218693476$V1),col="magenta")
lines(density(gd332341332$V1),col="brown")
lines(density(gd49175990$V1),col="yellow")
summary(gd49175990)
hist(t(gi.id49175990.gatc),breaks=100)
hist(t(gi.id49175990.gatc/gi.id49175990.gatc[1,1]),breaks=100)
plot(density(t(gi.id49175990.gatc/gi.id49175990.gatc[1,1])))
lines(density(t(gi.id332341332.gatc/gi.id332341332.gatc[1,1])),col="yellow")
lines(density(t(gi.id218693476.gatc/gi.id218693476.gatc[1,1])),col="brown")
lines(density(t(gi.id215485161.gatc/gi.id215485161.gatc[1,1])),col="magenta")
lines(density(t(gi.id15829254.gatc/gi15829254.id.gatc[1,1])),col="cyan")
lines(density(t(gi.id15829254.gatc/gi.id15829254.gatc[1,1])),col="cyan")
lines(density(t(gi.id157159467.gatc/gi.id157159467.gatc[1,1])),col="blue")
lines(density(t(gi.id117622295.gatc/gi.id117622295.gatc[1,1])),col="red")
lines(density(t(gi.id157154711.gatc/gi.id157154711.gatc[1,1])),col="green")
savehistory('gatcdensity.r')
